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- PDB-5b1b: Bovine heart cytochrome c oxidase in the fully reduced state at 1... -

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Basic information

Entry
Database: PDB / ID: 5b1b
TitleBovine heart cytochrome c oxidase in the fully reduced state at 1.6 angstrom resolution
Components(Cytochrome c oxidase subunit ...) x 13
KeywordsOXIDOREDUCTASE / respiratory chain / Proton pump / Heme
Function / homology
Function and homology information


TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / respiratory chain complex IV / regulation of oxidative phosphorylation / Respiratory electron transport / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase ...TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / respiratory chain complex IV / regulation of oxidative phosphorylation / Respiratory electron transport / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / enzyme regulator activity / central nervous system development / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I ...Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome C Oxidase; Chain G / Cytochrome c oxidase, subunit VIa / Cytochrome C Oxidase; Chain M / Cytochrome C Oxidase; Chain L / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit III, four-helix bundle / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain J / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome c oxidase subunit VIc / Cytochrome C oxidase chain VIIB / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / : / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / Cytochrome C oxidase subunit II, transmembrane domain superfamily / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Helix Hairpins - #70 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxins - blue copper proteins / Four Helix Bundle (Hemerythrin (Met), subunit A) / Cupredoxin / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Few Secondary Structures / Irregular / Alpha Horseshoe / Helix Hairpins / Arc Repressor Mutant, subunit A / Up-down Bundle / Immunoglobulin-like / Sandwich
Similarity search - Domain/homology
CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / Chem-PGV / PHOSPHATE ION / Chem-PSC / TRISTEAROYLGLYCEROL ...CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / Chem-PGV / PHOSPHATE ION / Chem-PSC / TRISTEAROYLGLYCEROL / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYano, N. / Muramoto, K. / Shimada, A. / Takemura, S. / Baba, J. / Fujisawa, H. / Mochizuki, M. / Shinzawa-Itoh, K. / Yamashita, E. / Tsukihara, T. / Yoshikawa, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Science, Education and Sports of the Republic of Croatia2247012 Japan
Japan Society for the Promotion of Science (JSPS)22370060 Japan
Japan Society for the Promotion of Science (JSPS)26291033 Japan
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle.
Authors: Yano, N. / Muramoto, K. / Shimada, A. / Takemura, S. / Baba, J. / Fujisawa, H. / Mochizuki, M. / Shinzawa-Itoh, K. / Yamashita, E. / Tsukihara, T. / Yoshikawa, S.
History
DepositionDec 1, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Oct 13, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / diffrn / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_sheet_range / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _pdbx_audit_support.funding_organization / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns_shell.number_unique_obs / _struct.pdbx_CASP_flag / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Model completeness
Details: The previous analysis had not assigned any ethylene glycol molecule used as cry-protectant. Sixty-two ethylene glycol molecules were located in the crystal and multiple structures were ...Details: The previous analysis had not assigned any ethylene glycol molecule used as cry-protectant. Sixty-two ethylene glycol molecules were located in the crystal and multiple structures were included in the residues from 380 to 385 of subunits A and N.
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_validate_chiral

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
E: Cytochrome c oxidase subunit 5A, mitochondrial
F: Cytochrome c oxidase subunit 5B, mitochondrial
G: Cytochrome c oxidase subunit 6A2, mitochondrial
H: Cytochrome c oxidase subunit 6B1
I: Cytochrome c oxidase subunit 6C
J: Cytochrome c oxidase subunit 7A1, mitochondrial
K: Cytochrome c oxidase subunit 7B, mitochondrial
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8B, mitochondrial
N: Cytochrome c oxidase subunit 1
O: Cytochrome c oxidase subunit 2
P: Cytochrome c oxidase subunit 3
Q: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
R: Cytochrome c oxidase subunit 5A, mitochondrial
S: Cytochrome c oxidase subunit 5B, mitochondrial
T: Cytochrome c oxidase subunit 6A2, mitochondrial
U: Cytochrome c oxidase subunit 6B1
V: Cytochrome c oxidase subunit 6C
W: Cytochrome c oxidase subunit 7A1, mitochondrial
X: Cytochrome c oxidase subunit 7B, mitochondrial
Y: Cytochrome c oxidase subunit 7C, mitochondrial
Z: Cytochrome c oxidase subunit 8B, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,063159
Polymers404,13326
Non-polymers44,930133
Water59,5043303
1
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
E: Cytochrome c oxidase subunit 5A, mitochondrial
F: Cytochrome c oxidase subunit 5B, mitochondrial
G: Cytochrome c oxidase subunit 6A2, mitochondrial
H: Cytochrome c oxidase subunit 6B1
I: Cytochrome c oxidase subunit 6C
J: Cytochrome c oxidase subunit 7A1, mitochondrial
K: Cytochrome c oxidase subunit 7B, mitochondrial
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8B, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,54080
Polymers202,06713
Non-polymers23,47367
Water23413
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: Cytochrome c oxidase subunit 1
O: Cytochrome c oxidase subunit 2
P: Cytochrome c oxidase subunit 3
Q: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
R: Cytochrome c oxidase subunit 5A, mitochondrial
S: Cytochrome c oxidase subunit 5B, mitochondrial
T: Cytochrome c oxidase subunit 6A2, mitochondrial
U: Cytochrome c oxidase subunit 6B1
V: Cytochrome c oxidase subunit 6C
W: Cytochrome c oxidase subunit 7A1, mitochondrial
X: Cytochrome c oxidase subunit 7B, mitochondrial
Y: Cytochrome c oxidase subunit 7C, mitochondrial
Z: Cytochrome c oxidase subunit 8B, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,52379
Polymers202,06713
Non-polymers21,45766
Water23413
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.606, 204.140, 177.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.992768, -0.004488, 0.119962), (-0.000227, -0.999229, -0.039256), (0.120046, -0.039, 0.992002)164.41495, 625.38745, 2.40745
3given(1), (1), (1)
4given(-0.993212, 0.000992, 0.116313), (-0.006027, -0.999059, -0.042943), (0.116161, -0.043353, 0.992284)163.28622, 626.74615, 4.34892
5given(1), (1), (1)
6given(-0.992508, -0.001076, 0.122176), (-0.003842, -0.999192, -0.040011), (0.12212, -0.04018, 0.991702)162.91132, 625.95697, 2.59309
7given(1), (1), (1)
8given(-0.993229, -0.003045, 0.116136), (6.4E-5, -0.999671, -0.025668), (0.116176, -0.025487, 0.992902)164.74612, 623.078, -1.28649
9given(1), (1), (1)
10given(-0.98936, -0.061405, 0.131893), (0.056003, -0.997448, -0.044288), (0.134276, -0.03643, 0.990274)180.11153, 618.70111, 0.23422
11given(1), (1), (1)
12given(-0.993498, -0.004825, 0.113747), (0.001198, -0.999489, -0.031932), (0.113843, -0.031588, 0.992996)166.07048, 623.698, 0.57206
13given(1), (1), (1)
14given(-0.992566, -0.004956, 0.12161), (-7.3E-5, -0.999146, -0.041308), (0.121711, -0.04101, 0.991718)164.1266, 625.80078, 2.87112
15given(1), (1), (1)
16given(-0.991113, 0.005847, 0.132896), (-0.011301, -0.999123, -0.040327), (0.132544, -0.04147, 0.990309)159.00999, 626.87878, 2.05259
17given(1), (1), (1)
18given(-0.994152, -0.021001, 0.105929), (0.017873, -0.999378, -0.03039), (0.106502, -0.028319, 0.993909)172.45477, 621.41284, 0.33541
19given(1), (1), (1)
20given(-0.993229, 0.001133, 0.11617), (-0.006452, -0.998947, -0.045427), (0.115996, -0.045869, 0.99219)163.64609, 627.29059, 4.84758
21given(1), (1), (1)
22given(-0.993373, 0.006479, 0.114751), (-0.009325, -0.999662, -0.024282), (0.114555, -0.025191, 0.993098)161.88466, 624.284, -1.32942
23given(1), (1), (1)
24given(-0.992644, -0.01651, 0.11994), (0.012597, -0.999366, -0.033314), (0.120414, -0.031558, 0.992222)167.97585, 622.35315, 0.04377
25given(1), (1), (1)
26given(-0.991639, -0.018693, 0.127682), (0.013369, -0.99901, -0.042428), (0.128349, -0.040366, 0.990907)166.92584, 623.85236, 1.60161

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Components

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Cytochrome c oxidase subunit ... , 13 types, 26 molecules ANBOCPDQERFSGTHUIVJWKXLYMZ

#1: Protein Cytochrome c oxidase subunit 1 / / Cytochrome c oxidase polypeptide I


Mass: 57093.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00396, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / / Cytochrome c oxidase polypeptide II


Mass: 26068.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P68530, cytochrome-c oxidase
#3: Protein Cytochrome c oxidase subunit 3 / / Cytochrome c oxidase polypeptide III


Mass: 29725.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00415, cytochrome-c oxidase
#4: Protein Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / / Cytochrome c oxidase polypeptide IV / Cytochrome c oxidase subunit IV isoform 1 / COX IV-1


Mass: 16913.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00423
#5: Protein Cytochrome c oxidase subunit 5A, mitochondrial / / Cytochrome c oxidase polypeptide Va


Mass: 12083.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00426
#6: Protein Cytochrome c oxidase subunit 5B, mitochondrial / / Cytochrome c oxidase polypeptide VIa / Cytochrome c oxidase polypeptide Vb


Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00428
#7: Protein Cytochrome c oxidase subunit 6A2, mitochondrial / / Cytochrome c oxidase polypeptide VIa-heart / COXVIAH / Cytochrome c oxidase polypeptide VIb


Mass: 9452.687 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07471
#8: Protein Cytochrome c oxidase subunit 6B1 / / Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase ...Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase subunit VIb isoform 1 / COX VIb-1


Mass: 9411.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00429
#9: Protein Cytochrome c oxidase subunit 6C / / Cytochrome c oxidase polypeptide VIc / Cytochrome c oxidase subunit STA


Mass: 8537.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P04038
#10: Protein Cytochrome c oxidase subunit 7A1, mitochondrial / / Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c ...Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c oxidase subunit VIIa-H / Cytochrome c oxidase subunit VIIa-muscle / Cytochrome c oxidase subunit VIIa-M


Mass: 6553.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07470
#11: Protein/peptide Cytochrome c oxidase subunit 7B, mitochondrial / / Cytochrome c oxidase polypeptide VIIb / IHQ


Mass: 5442.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13183
#12: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial / / Cytochrome c oxidase polypeptide VIIIA / Cytochrome c oxidase polypeptide VIIc


Mass: 5362.319 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00430
#13: Protein/peptide Cytochrome c oxidase subunit 8B, mitochondrial / / Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c ...Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c oxidase subunit 8H / IX / VIIIb


Mass: 4738.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P10175

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Sugars , 1 types, 23 molecules

#24: Sugar...
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 23
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 15 types, 3413 molecules

#14: Chemical
ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#15: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#16: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#17: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#18: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#19: Chemical
ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL / Stearin


Mass: 891.480 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C57H110O6
#20: Chemical ChemComp-PSC / (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 2-LINOLEOYL-1-PALMITOYL-SN-GYCEROL-3-PHOSPHOCHOLINE / Phosphatidylcholine


Mass: 759.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H81NO8P / Comment: phospholipid*YM
#21: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 62 / Source method: obtained synthetically / Formula: C2H6O2
#22: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#23: Chemical
ChemComp-CHD / CHOLIC ACID / Cholic acid


Mass: 408.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40O5
#25: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#26: Chemical
ChemComp-PEK / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE / PHOSPHATIDYLETHANOLAMINE / 2-ARACHIDONOYL-1-STEAROYL-SN-GLYCEROL-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 768.055 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C43H78NO8P / Comment: phospholipid*YM
#27: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#28: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#29: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3303 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.36 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 6.8 / Details: PEG 4000, Sodium phosphate, Decylmaltoside

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Data collection

DiffractionMean temperature: 50 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→200 Å / Num. obs: 850991 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 25.5
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.74 / Num. unique obs: 28158 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DYR

2dyr


Resolution: 1.6→39.897 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 20.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.191 41978 5.02 %RANDOM
Rwork0.1684 ---
obs0.1696 836451 97.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→39.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28498 0 2305 3303 34106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01931928
X-RAY DIFFRACTIONf_angle_d1.62642916
X-RAY DIFFRACTIONf_dihedral_angle_d15.16818620
X-RAY DIFFRACTIONf_chiral_restr0.114527
X-RAY DIFFRACTIONf_plane_restr0.0125100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.271814080.236826295X-RAY DIFFRACTION97
1.6182-1.63720.244213830.223826316X-RAY DIFFRACTION97
1.6372-1.65720.22613920.212826285X-RAY DIFFRACTION98
1.6572-1.67820.234613960.208426371X-RAY DIFFRACTION98
1.6782-1.70020.212514760.199226290X-RAY DIFFRACTION98
1.7002-1.72350.212514130.19426322X-RAY DIFFRACTION98
1.7235-1.74820.219414350.189726260X-RAY DIFFRACTION97
1.7482-1.77430.205113860.180126387X-RAY DIFFRACTION97
1.7743-1.8020.205613530.181426314X-RAY DIFFRACTION97
1.802-1.83150.208313160.180326427X-RAY DIFFRACTION97
1.8315-1.86310.210313680.180926198X-RAY DIFFRACTION97
1.8631-1.8970.212914040.17926233X-RAY DIFFRACTION97
1.897-1.93350.204214460.173926244X-RAY DIFFRACTION97
1.9335-1.97290.204213330.173126370X-RAY DIFFRACTION97
1.9729-2.01580.199413750.169326490X-RAY DIFFRACTION98
2.0158-2.06270.196614350.168526463X-RAY DIFFRACTION98
2.0627-2.11430.195214100.167626444X-RAY DIFFRACTION98
2.1143-2.17150.194814480.16826194X-RAY DIFFRACTION97
2.1715-2.23540.191413820.165426259X-RAY DIFFRACTION97
2.2354-2.30750.184114080.165626135X-RAY DIFFRACTION96
2.3075-2.390.191813170.164126207X-RAY DIFFRACTION96
2.39-2.48560.181113500.1626225X-RAY DIFFRACTION96
2.4856-2.59870.183413490.156526276X-RAY DIFFRACTION97
2.5987-2.73570.183613490.152926573X-RAY DIFFRACTION97
2.7357-2.90710.171914130.155926584X-RAY DIFFRACTION98
2.9071-3.13150.183414390.160326773X-RAY DIFFRACTION98
3.1315-3.44640.186713970.16326984X-RAY DIFFRACTION99
3.4464-3.94480.181514380.158527229X-RAY DIFFRACTION99
3.9448-4.96850.171114550.154227393X-RAY DIFFRACTION99
4.9685-39.8970.204915040.190227932X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.26930.0225-0.06650.11530.00340.2970.0010.04150.02120.00540.01360.01840.0162-0.04850.01930.09570.0047-0.00750.07550.00970.08460.977305.95197.999
20.38530.0820.07770.203-0.04650.35560.01410.1247-0.06190.02220.017-0.0782-0.02990.10430.05040.1019-0.0096-0.00040.1164-0.03260.1487126.125312.021194.057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )A1 - 514
2X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )C4 - 261
3X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )B1 - 227
4X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )E5 - 109
5X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )D4 - 147
6X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )G1 - 84
7X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )F1 - 98
8X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )I1 - 73
9X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )H7 - 85
10X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )K6 - 54
11X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )J1 - 58
12X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )M1 - 43
13X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )L2 - 47
14X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )O1 - 227
15X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )N1 - 514
16X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )Q4 - 147
17X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )P4 - 261
18X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )S1 - 98
19X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )R5 - 109
20X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )U7 - 85
21X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )T1 - 84
22X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )W1 - 58
23X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )V1 - 73
24X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )Y2 - 47
25X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )X6 - 54
26X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )Z1 - 43

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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